Make provisioning scripts run in unprivileged mode + more (#17)

* Make provisioning scripts run in unprivileged mode + more

* Move install-vscode to home

To declutter the Desktop and avoid users just randomly clicking on it

* Enable object files clean-up by default

* Format files (mostly endlines)

* install-su2.sh: group echo commands (shellcheck)

* Move the cleanup objects step to post-install

* Move cleanup steps to cleanup.sh

README.md

@@ -23,6 +23,7 @@ Ready-to-use boxes are available on [Vagrant Cloud](https://app.vagrantup.com/pr
 You can afterwards also see and manage the produced VM in VirtualBox.
 
 A few things you may need:
+
 - The username and password are `vagrant`/`vagrant`
 - The keyboard layout is US English (QWERTY). You can change this in [`install-basics.sh`](./install-basics.sh) or through the keyboard setting shortcut on `~/Desktop`.
 - Find scripts to install additional software on `~/Desktop/shared`.
@@ -40,6 +41,7 @@ A few things you may need:
 ## What is included?
 
 This box is based on the [bento/ubuntu-20.04](https://github.com/chef/bento/blob/master/packer_templates/ubuntu/ubuntu-20.04-amd64.json) base box and installs:
+
 - Xubuntu-core (Xfce desktop environment) and related tools
 - VirtualBox guest additions
 - Terminator (a nice split-window terminal emulator, find it in `Applications > System`)
@@ -49,14 +51,15 @@ This box is based on the [bento/ubuntu-20.04](https://github.com/chef/bento/blob
 - preCICE config visualizer latest from the master branch
 - preCICE Python bindings
 - OpenFOAM v2012 and the OpenFOAM-preCICE adapter
-- deal.II 9.2 from the official backports and the deal.II-preCICE adapter (you still need to copy the compiled executables wherever you need them)
+- deal.II 9.2 from the official backports and the deal.II-preCICE adapter
 - CalculiX 2.16 from source and the CalculiX-preCICE adapter
 - FEniCS latest from the FEniCS PPA and the FEniCS-preCICE adapter
 - Nutils latest from PIP
 - SU2 6.0.0 and the SU2-preCICE adapter from source
 - Paraview from the official binaries
 
-It then adds on the `/home/vagrant/Desktop`:
+It then adds on the `/home/vagrant/`:
+
 - The preCICE examples (solverdummies), including a copy of the Python solverdummy.
 - The preCICE tutorials from the `precice/tutorials`
 

Vagrantfile

@@ -26,32 +26,35 @@ Vagrant.configure("2") do |config|
   end
 
   # Install a desktop environment and basic tools
-  config.vm.provision "shell", path: "provisioning/install-basics.sh"
+  config.vm.provision "shell", path: "provisioning/install-basics.sh", privileged: false
 
   # Install common development tools
-  config.vm.provision "shell", path: "provisioning/install-devel.sh"
+  config.vm.provision "shell", path: "provisioning/install-devel.sh", privileged: false
 
   # Install preCICE
-  config.vm.provision "shell", path: "provisioning/install-precice.sh"
+  config.vm.provision "shell", path: "provisioning/install-precice.sh", privileged: false
 
   # Install solvers, adapters, and related tools
-  config.vm.provision "shell", path: "provisioning/install-config-visualizer.sh"
-  config.vm.provision "shell", path: "provisioning/install-openfoam.sh"
-  config.vm.provision "shell", path: "provisioning/install-dealii.sh"
-  config.vm.provision "shell", path: "provisioning/install-calculix.sh"
-  config.vm.provision "shell", path: "provisioning/install-fenics.sh"
-  config.vm.provision "shell", path: "provisioning/install-nutils.sh"
-  config.vm.provision "shell", path: "provisioning/install-su2.sh"
-  config.vm.provision "shell", path: "provisioning/install-paraview.sh"
+  config.vm.provision "shell", path: "provisioning/install-config-visualizer.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-openfoam.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-dealii.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-calculix.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-fenics.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-nutils.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-su2.sh", privileged: false
+  config.vm.provision "shell", path: "provisioning/install-paraview.sh", privileged: false
 
   # Post-installation steps
-  config.vm.provision "shell", path: "provisioning/post-install.sh"
-  config.vm.provision "file", source: "provisioning/install-vscode.sh", destination: "~/Desktop/install-vscode.sh"
+  config.vm.provision "shell", path: "provisioning/post-install.sh", privileged: false
+  config.vm.provision "file", source: "provisioning/install-vscode.sh", destination: "~/install-vscode.sh"
+  config.vm.provision "file", source: "provisioning/get-started.desktop", destination: "~/Desktop/get-started.desktop"
 
   # Pre-packaging steps
+  # config.vm.provision "shell", path: "provisioning/cleanup.sh", privileged: false
   # Add the default Vagrant insecure public key to the authorized keys
   config.vm.provision "file", source: "provisioning/vagrant.pub", destination: "~/.ssh/vagrant.pub"
   config.vm.provision "shell", inline: <<-SHELL
     cat /home/vagrant/.ssh/vagrant.pub >> /home/vagrant/.ssh/authorized_keys
   SHELL
+
 end

provisioning/cleanup.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -ex
+
+# Cleanup the APT cache to save space
+sudo apt-get clean
+
+# Cleanup all object files from compilation
+find /home/vagrant/ -type f -name '*.o' -exec rm -fv {} \;

provisioning/get-started.desktop

@@ -0,0 +1,6 @@
+[Desktop Entry]
+Encoding=UTF-8
+Name=Get started
+Type=Link
+URL=https://precice.org/installation-vm.html
+Icon=text-html

provisioning/install-basics.sh

@@ -1,11 +1,9 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # We (may) need the multiverse repository for the VBox Guest Additions
 sudo apt-add-repository multiverse
-apt-get update
+sudo apt-get update
 sudo apt-get upgrade -qy
 
 # Install the Xfce desktop environment and basic applications
@@ -15,16 +13,14 @@ sudo apt-get install -y thunar xfce4-terminal terminator bash-completion tree ev
 # Install the VirtualBox guest additions
 sudo apt-get install -y virtualbox-guest-dkms virtualbox-guest-utils virtualbox-guest-x11
 
-# Create /home/${USER}/desktop
-sudo -u ${USER} mkdir -p /home/${USER}/Desktop
-chown ${USER}:${USER} /home/${USER}/Desktop
+# Create Desktop
+mkdir -p ~/Desktop
 
 # Use US-English keyboard layout
 L='us' && sudo sed -i 's/XKBLAYOUT=\"\w*"/XKBLAYOUT=\"'$L'\"/g' /etc/default/keyboard
 # Add a shortcut to the keyboard options on the Desktop
-cp /usr/share/applications/xfce-keyboard-settings.desktop /home/${USER}/Desktop/
-chmod +x /home/${USER}/Desktop/xfce-keyboard-settings.desktop
-chown ${USER}:${USER} /home/${USER}/Desktop/xfce-keyboard-settings.desktop
+cp /usr/share/applications/xfce-keyboard-settings.desktop ~/Desktop/
+chmod +x ~/Desktop/xfce-keyboard-settings.desktop
 
 # Set a hostname
 echo "precicevm" | sudo tee /etc/hostname

provisioning/install-calculix.sh

@@ -1,23 +1,22 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Install dependencies
 sudo apt-get install -y libarpack2-dev libspooles-dev libyaml-cpp-dev
 
-# Install CalculiX 
-cd /home/${USER}/
+# Install CalculiX
 wget --quiet http://www.dhondt.de/ccx_2.16.src.tar.bz2
-tar xvjf ccx_2.16.src.tar.bz2 
+tar xvjf ccx_2.16.src.tar.bz2
 
 # Get the CalculiX-preCICE adapter
 if [ ! -d "calculix-adapter/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git
+    git clone --depth=1 --branch master https://github.com/precice/calculix-adapter.git
 fi
-cd calculix-adapter
-git pull
-sudo -u ${USER} -s bash -c "make -j 2"
+(
+    cd calculix-adapter
+    git pull
+    make -j 2
+)
 
 # Add the CalculiX adapter to PATH
-echo "export PATH=\"/home/${USER}/calculix-adapter/bin:\${PATH}\"" >> /home/${USER}/.bashrc
+echo "export PATH=\"~/calculix-adapter/bin:\${PATH}\"" >>~/.bashrc

provisioning/install-config-visualizer.sh

@@ -1,20 +1,18 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Get the config-visualizer from GitHub
 if [ ! -d "config-visualizer/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/config-visualizer.git
+    git clone --depth=1 --branch master https://github.com/precice/config-visualizer.git
 fi
-sudo -u ${USER} -s bash -c "pip3 install --user -e config-visualizer"
+pip3 install --user -e config-visualizer
 
 # Add the config-visualizer to PATH
-echo "export PATH=\"/home/${USER}/config-visualizer/bin:${PATH}\"" >> /home/${USER}/.bashrc
+echo "export PATH=\"~/config-visualizer/bin:\${PATH}\"" >>~/.bashrc
 
 # By default, there is no `python` executable, there is only `python3`,
 # which causes issues to the config-visualizer
-apt-get install -y python-is-python3
+sudo apt-get install -y python-is-python3
 
 # Install graphviz, which provides dot, an almost required package to make this useful
-apt-get install -y graphviz
+sudo apt-get install -y graphviz

provisioning/install-dealii.sh

@@ -1,24 +1,20 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Install deal.II from the deal.II 9.2.0 backports PPA
 sudo add-apt-repository ppa:ginggs/deal.ii-9.2.0-backports
 sudo apt-get update
 sudo apt-get install -y libdeal.ii-dev
 
 # Get the deal.II-preCICE adapter
 if [ ! -d "dealii-adapter/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/dealii-adapter.git
+    git clone --depth=1 --branch master https://github.com/precice/dealii-adapter.git
 fi
-cd dealii-adapter
-git pull
-
-# Build the linear elasticity solver
-cd linear_elasticity
-sudo -u ${USER} -s bash -c "cmake . && make -j 2"
+(
+    cd dealii-adapter
+    git pull
+    cmake . && make -j 2
+)
 
-# Build the nonlinear elasticity solver
-cd ../nonlinear_elasticity
-sudo -u ${USER} -s bash -c "cmake . && make -j 2"
+# Add the deal.II adapter to PATH
+echo "export PATH=\"~/dealii-adapter:\${PATH}\"" >>~/.bashrc

provisioning/install-devel.sh

@@ -1,6 +1,6 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-sudo apt-get install -y git cmake cmake-curses-gui
+sudo apt-get install -y build-essential git cmake cmake-curses-gui
 
-sudo apt-get install -y nano vim gedit
+sudo apt-get install -y nano vim gedit

provisioning/install-fenics.sh

@@ -1,15 +1,11 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Install FEniCS from APT
-apt-get install -y software-properties-common
-add-apt-repository -y ppa:fenics-packages/fenics
-apt-get -y update
-apt-get -y install --no-install-recommends fenics
+sudo apt-get install -y software-properties-common
+sudo add-apt-repository -y ppa:fenics-packages/fenics
+sudo apt-get -y update
+sudo apt-get -y install --no-install-recommends fenics
 
 # Install the FEniCS-preCICE adapter from PIP
-sudo -u ${USER} pip3 install --user fenicsprecice
-# Remove a conflicting with the adapter package
-pip3 uninstall -y fenics-ufl
+pip3 install --user fenicsprecice

provisioning/install-nutils.sh

@@ -1,7 +1,5 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Install Nutils from PIP (we will also need matplotlib in our examples)
-sudo -u ${USER} pip3 install --user matplotlib nutils
+pip3 install --user matplotlib nutils

provisioning/install-openfoam.sh

@@ -1,21 +1,22 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Add the signing key, add the repository, update:
 wget -q -O - https://dl.openfoam.com/add-debian-repo.sh | sudo bash
 
 # Install OpenFOAM v2012:
 sudo apt-get install -y openfoam2012-dev
-openfoam-selector --set openfoam2012 --system
-# todo: Somehow the openfoam-selector is not enough - the binaries are discoverable, but the libraries not. Remedy:
-echo "source /etc/profile.d/openfoam-selector.sh" >> /home/vagrant/.bashrc
+# Enable OpenFOAM by default and apply now:
+echo ". /usr/lib/openfoam/openfoam2012/etc/bashrc" >> ~/.bashrc
+# shellcheck source=/dev/null
+# . /usr/lib/openfoam/openfoam2012/etc/bashrc
 
 # Get the OpenFOAM-preCICE adapter
 if [ ! -d "openfoam-adapter/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/openfoam-adapter.git
+    git clone --depth=1 --branch master https://github.com/precice/openfoam-adapter.git
 fi
-cd openfoam-adapter
-git pull
-sudo -u ${USER} -s bash -l ./Allwmake
+(
+    cd openfoam-adapter
+    git pull
+    ./Allwmake
+)

provisioning/install-paraview.sh

@@ -1,14 +1,11 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 if [ ! -d "paraview" ]; then
     mkdir paraview
     PARAVIEW_URL="https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.8&type=binary&os=Linux&downloadFile=ParaView-5.8.1-MPI-Linux-Python3.7-64bit.tar.gz"
-    wget --no-check-certificate --quiet -O - ${PARAVIEW_URL} | tar -xz -C paraview
-    ln -sf /home/${USER}/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin/paraview /home/${USER}/Desktop/
-    chown ${USER}:${USER} /home/${USER}/Desktop/paraview
+    wget --no-check-certificate --quiet -O - "${PARAVIEW_URL}" | tar -xz -C paraview
+    ln -sf ~/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin/paraview ~/Desktop/
     # Add ParaView to PATH
-    echo "export PATH=\"/home/${USER}/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin:\${PATH}\"" >> /home/${USER}/.bashrc
-fi
+    echo "export PATH=\"~/paraview/ParaView-5.8.1-MPI-Linux-Python3.7-64bit/bin:\${PATH}\"" >>~/.bashrc
+fi

provisioning/install-precice.sh

@@ -1,42 +1,42 @@
-#!/bin/sh
+#!/usr/bin/env bash
 set -ex
 
-USER="vagrant"
-
 # Get preCICE dependencies
-apt-get install -y build-essential cmake libeigen3-dev libxml2-dev libboost-all-dev petsc-dev python3-dev python3-numpy
+sudo apt-get install -y cmake libeigen3-dev libxml2-dev libboost-all-dev petsc-dev python3-dev python3-numpy
 
 # Get preCICE from GitHub:
 # - Always get the latest master, no need for versioning
 # - Build in Debug mode, so that users can report bugs
 if [ ! -d "precice/" ]; then
-    sudo -u ${USER} git clone --depth=1 --branch master https://github.com/precice/precice.git
+    git clone --depth=1 --branch master https://github.com/precice/precice.git
+fi
+(
     cd precice
     git pull
-    sudo -u ${USER} -s bash -c "mkdir build && cd build/ && rm -fv *.deb && cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Debug .. && make -j 2  && make package"
-    apt-get install -y ./build/libprecice2_*.deb
-fi
+    mkdir -p build && cd build/
+    cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Debug -Wno-dev ..
+    make -j 2
+    rm -fv ./*.deb && make package
+    sudo apt-get install -y ./libprecice2_*.deb
+)
 
-# Collect examples
-cd /home/${USER}/Desktop
-    sudo -u ${USER} cp -r /usr/share/precice/examples/ .
-    if [ ! -d "tutorials/" ]; then
-        sudo -u ${USER} git clone --branch master https://github.com/precice/tutorials.git
-    fi
-cd -
+# Collect examples and tutorials
+cp -r /usr/share/precice/examples/ ./precice-examples
+if [ ! -d "tutorials/" ]; then
+    git clone --depth=1 --branch master https://github.com/precice/tutorials.git
+    ln -sf ~/tutorials ~/Desktop/
+fi
 
 ### OPTIONAL - preCICE Python bindings and Python example
 # Get PIP and the preCICE Python bindings
 sudo apt-get install -y python3-pip
-sudo -u ${USER} pip3 install --upgrade pip
-sudo -u ${USER} pip3 install --user pyprecice
+pip3 install --upgrade pip
+pip3 install --user pyprecice
 
 # Get the Python solverdummy into the examples
-cd /home/${USER}/Desktop
-    if [ ! -d "python-bindings/" ]; then
-        sudo -u ${USER} git clone --branch master https://github.com/precice/python-bindings.git
-    fi
-    sudo -u ${USER} cp -r python-bindings/solverdummy/ examples/solverdummies/python/
-    sudo rm -r python-bindings
-cd -
-###
+if [ ! -d "python-bindings/" ]; then
+    git clone --depth=1 --branch master https://github.com/precice/python-bindings.git
+fi
+cp -r python-bindings/solverdummy/ precice-examples/solverdummies/python/
+rm -r python-bindings
+###